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Crystal Structure of UDP-N-acetylmuramic acid:L-alanine ligase (MurC) in Complex with UMA and ANP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P31 PDB ENTRY 1P31
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 PEG 4000, isopropanol, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.58 52.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.92 α = 90 b = 87.328 β = 104.86 c = 86.113 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2002-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.0 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.7 25 96.6 0.046 13.4 4.31 117454 113461 2 2 20.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.76 90.5 0.542 2.47 4.5 10574
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1P31 1.7 25 107740 107740 5691 96.53 0.16953 0.16953 0.16822 0.1699 0.19436 RANDOM 14.505
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.46 -0.44 1.4 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.46 r_scangle_it 2.107 r_scbond_it 1.377 r_angle_refined_deg 1.129 r_mcangle_it 0.642 r_mcbond_it 0.333 r_nbd_refined 0.189 r_symmetry_hbond_refined 0.13 r_symmetry_vdw_refined 0.125 r_xyhbond_nbd_refined 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.46 r_scangle_it 2.107 r_scbond_it 1.377 r_angle_refined_deg 1.129 r_mcangle_it 0.642 r_mcbond_it 0.333 r_nbd_refined 0.189 r_symmetry_hbond_refined 0.13 r_symmetry_vdw_refined 0.125 r_xyhbond_nbd_refined 0.094 r_chiral_restr 0.084 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7099 Nucleic Acid Atoms Solvent Atoms 791 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing